About Swiss TPH
The Swiss Tropical and Public Health Institute (Swiss TPH) is a world-leading institute in global health focusing on low- and middle-income countries. Affiliated with the University of Basel, Swiss TPH combines research, education, and services at local, national, and international levels. It has 950 staff from 95 nations working on infectious and non-communicable diseases, environment, society and health, and health systems.
Department Description
The Department of Medical Parasitology and Infection Biology (MPI) investigates pathogen biology and transmission to inform development of diagnostics, treatments, and vaccines for diseases such as malaria, tuberculosis, schistosomiasis, Chagas, and other neglected tropical diseases.
Position Overview
This project investigates how hospital environments and patient compartments contribute to antimicrobial resistance (AMR) gene evolution, persistence, and transmission. Using high-throughput sequencing and data analysis in hospitals across Guinea-Bissau, Nigeria, and Côte d’Ivoire, the project reconstructs AMR transmission pathways and identifies drivers of resistance at the patient-environment interface.
Your various responsibilities include:
- Design and conduct longitudinal phylogenetic and ecological analyses of microbial communities to identify AMR transmission routes across reservoirs
- Perform sequencing experiments on Illumina and Nanopore platforms; implement hybrid metagenomics assembly using HPC infrastructure
- Coordinate and supervise clinical and environmental sample collection; contribute to sampling strategy and SOP development
- Contribute to capacity building through local training workshops with West African partners
- Publish high-impact scientific articles and participate in project reporting and dissemination
You should have the following experience and skills:
- PhD in microbial ecology, molecular microbiology, microbiome research, or related field
- Proficiency or motivation in bioinformatics; HPC and metagenomics pipeline experience preferred
- Experience with next-generation sequencing; Illumina and/or Nanopore and meta-omics a plus
- Strong organizational skills, lab detail orientation, and ability to work independently
- Willingness for short-term fieldwork in Guinea-Bissau, Nigeria, and Côte d’Ivoire
- Solid publication record for career stage with recent first-author papers
What we offer:
- Meaningful work in an international environment
- Committed and motivated team with short decision paths
- State-of-the-art workplace at BaseLink site in Allschwil
- Diverse inspiring encounters
- Attractive employment conditions, versatile training, and mentoring
Job conditions:
- Start Date: as soon as possible
- Duration: 2 years
- Percentage: 80-100%
- Location: Allschwil, Switzerland
- Travel: Possibly 10-20% at project start
- Internal job title: Postdoctoral Scientific Collaborator